Align arginine deiminase (EC 3.5.3.6) (characterized)
to candidate Echvi_0366 Echvi_0366 Uncharacterized protein conserved in bacteria containing a pentein-type domain
Query= reanno::WCS417:GFF3434 (308 letters) >FitnessBrowser__Cola:Echvi_0366 Length = 314 Score = 278 bits (711), Expect = 1e-79 Identities = 140/304 (46%), Positives = 199/304 (65%), Gaps = 3/304 (0%) Query: 2 QTTNTVLMIRPARFAFNPDTAINNRFQRQPLDPLGA-QQKALEEFDGYVDTLRRHGVEVL 60 QTT+T+LM+RPA F FNP+TA++N +Q++ QQ A +EFD V LR+ GV V+ Sbjct: 4 QTTSTILMVRPAAFGFNPETALDNSYQQEDARSTAEIQQVAEQEFDDVVALLRKKGVRVI 63 Query: 61 VVQDTPAPHTPDSIFPNNWWSSHADGSLVLYPMEGQNRRLERNKGVLQVLE-QRFAINST 119 V QD+P P PD++FPNNW+S+H DG L+ YPM RR ER K ++ +L + F ++ Sbjct: 64 VAQDSPLPVKPDAVFPNNWFSTHEDGRLLWYPMLSPVRRKERRKDLVDILGVEGFRVDEL 123 Query: 120 IDLSHLEQQNIFLEGTGSMVLDRQHRISYACHSGRTHQDALRQFAERLDYQLCVFHAV-D 178 +D + E FLE TGSMVLDR+H+I+YAC S RTH + L F +DYQ+ F AV Sbjct: 124 VDFTFFEDAQQFLESTGSMVLDREHKIAYACLSERTHPEPLHYFERLMDYQVVSFRAVHS 183 Query: 179 RHHAPIYHSNVMMSVGRDLSVVCLQALPDASERQGLERSLRDTGKDILALDFDQLEGFAG 238 P+YH+NVMM VG L+VVCL ++ S +Q ++ SL +GK ++ + Q FAG Sbjct: 184 SSKIPVYHTNVMMHVGSQLAVVCLDSIVGKSVKQWVKESLEGSGKKVVPITIPQKFAFAG 243 Query: 239 NMLEIHDRDGQPLLVMSASAWGALQPAQRQHVERHTRPVVVNIDNIERIGGGSARCMLAE 298 NMLE+ +G+ + VMS +A+ +L+ QRQ +E++T VV I IE++GGG RCM+AE Sbjct: 244 NMLEVDGENGKKITVMSETAYQSLKQGQRQVIEKYTEVVVAKIPTIEKVGGGGVRCMMAE 303 Query: 299 VHLP 302 + LP Sbjct: 304 IFLP 307 Lambda K H 0.322 0.135 0.408 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 275 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 308 Length of database: 314 Length adjustment: 27 Effective length of query: 281 Effective length of database: 287 Effective search space: 80647 Effective search space used: 80647 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory